Kdm8 lysine demethylase 8 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Kdm8provided by RGD
Official Full Name: lysine demethylase 8provided by RGD
Primary source: RGD:1304823
See related: Ensembl:ENSRNOG00000015180 AllianceGenome:RGD:1304823
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Jmjd5; RGD1304823
Summary: Predicted to enable several functions, including 2-oxoglutarate-dependent dioxygenase activity; methylated histone binding activity; and peptidase activity. Predicted to be involved in several processes, including histone H3-K36 demethylation; protein destabilization; and regulation of gene expression. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human KDM8 (lysine demethylase 8). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Heart (RPKM 96.3), Muscle (RPKM 89.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q36

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (189444527..189459507)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (180013969..180028829)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (196838460..196854192)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables aminopeptidase activity	IEA Inferred from Electronic Annotation more info
enables aminopeptidase activity	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables endopeptidase activity	IEA Inferred from Electronic Annotation more info
enables endopeptidase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K36 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K36 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K36 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables molecular_function	ND No biological Data available more info
enables p53 binding	IEA Inferred from Electronic Annotation more info
enables p53 binding	ISO Inferred from Sequence Orthology more info
enables peptidyl-arginine 3-dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables peptidyl-arginine 3-dioxygenase activity	ISO Inferred from Sequence Orthology more info
enables peptidyl-arginine 3-dioxygenase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in G2/M transition of mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in G2/M transition of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in G2/M transition of mitotic cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in biological_process	ND No biological Data available more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in circadian regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in circadian regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in fibroblast proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within fibroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein destabilization	IEA Inferred from Electronic Annotation more info
involved_in protein destabilization	ISO Inferred from Sequence Orthology more info
involved_in protein destabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in regulation of signal transduction by p53 class mediator	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of signal transduction by p53 class mediator	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cellular_component	ND No biological Data available more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: bifunctional peptidase and arginyl-hydroxylase JMJD5

Names: L-arginine (3R)-hydroxylase KDM8; arginyl C3-hydroxylase KDM8; jmjC domain-containing protein 5; jumonji C domain-containing protein 5; jumonji domain containing 5; jumonji domain-containing protein 5; lysine (K)-specific demethylase 8; lysine-specific demethylase 8

NP_001032273.1

EC 1.14.11.73

XP_063119293.1

EC 1.14.11.73

XP_063119297.1

EC 1.14.11.73

XP_063119299.1

EC 1.14.11.73

XP_063119307.1

EC 1.14.11.73

XP_063119308.1

EC 1.14.11.73

XP_063119309.1

EC 1.14.11.73

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001037196.1 → NP_001032273.1 bifunctional peptidase and arginyl-hydroxylase JMJD5

See identical proteins and their annotated locations for NP_001032273.1

Status: PROVISIONAL

Source sequence(s)

BC100627

UniProtKB/Swiss-Prot

Q497B8

Related

ENSRNOP00000020388.4, ENSRNOT00000020388.6

Conserved Domains (1) summary

pfam13621
Location:189 → 414

Cupin_8; Cupin-like domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

189444527..189459507

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063263229.1 → XP_063119299.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2
XM_063263223.1 → XP_063119293.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X1

UniProtKB/TrEMBL

A6I912, G3V7X6
XM_063263227.1 → XP_063119297.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2
XM_063263237.1 → XP_063119307.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X3
XM_063263238.1 → XP_063119308.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4
XM_063263239.1 → XP_063119309.1 bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4